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Unverified Commit 3ef12991 authored by Zane Beckwith's avatar Zane Beckwith Committed by GitHub
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modeller: Convey bond info when adding Modellers (#4113) 


Co-authored-by: default avatarZane Beckwith <zane.beckwith@sandboxquantum.com>
parent add2bbee
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wrappers/python/openmm/app/modeller.py
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...@@ -117,7 +117,7 @@ class Modeller(object): ...@@ -117,7 +117,7 @@ class Modeller(object):
newAtoms[atom] = newAtom newAtoms[atom] = newAtom
newPositions.append(deepcopy(self.positions[atom.index])) newPositions.append(deepcopy(self.positions[atom.index]))
for bond in self.topology.bonds(): for bond in self.topology.bonds():
newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]]) newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]], bond.type, bond.order)
# Add the new model # Add the new model
...@@ -131,7 +131,7 @@ class Modeller(object): ...@@ -131,7 +131,7 @@ class Modeller(object):
newAtoms[atom] = newAtom newAtoms[atom] = newAtom
newPositions.append(deepcopy(addPositions[atom.index])) newPositions.append(deepcopy(addPositions[atom.index]))
for bond in addTopology.bonds(): for bond in addTopology.bonds():
newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]]) newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]], bond.type, bond.order)
self.topology = newTopology self.topology = newTopology
self.positions = newPositions self.positions = newPositions
......
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